Two genes, IA-1 and IA-2, are the focus of our study. We determined the promoter region of IA-1 gene by transient transfection assay. These experiments showed that a 506 bp upstream sequence was sufficient for maximal expression of a reporter gene. Multiple known regulatory elements were found within this region including three E boxes and a clustered Sp-1 site. The promoter region of the IA-1 gene was located from -111 bp to +26 bp and displayed cell-specificity. Several promoter-binding nuclear factors specific for pituitary tumor and insulinoma cells were identified suggesting that they might be involved in the cell-specific expression of IA-1. IA-2 is a 105,874 kDa transmembrane protein that belongs to the protein tyrosine phosphatase family. We tested the reactivity of sera from patients with IDDM using full-length cDNA clone of IA-2 in a rabbit reticulocyte transcription/translation system. One hundred coded sera were tested, 50 from patients with newly diagnosed IDDM and 50 from age- matched normal controls. Sixty-six percent of the sera from diabetics, but none of the sera from controls, reacted with IA-2. A prospective study of IA-2 autoantigen (12 years duration) in 33 non-diabetic identical twins of IDDM probands and 38 controls showed that 11 twins developed IDDM. Ten of 11 prediabetic twins developed autoantibodies to IA-2 many years before the onset of IDDM, while only one of the 22 remaining non- diabetic twins developed autoantibodies to IA-2. Autoantibodies to IA-2 were detected in prediabetic sera more frequently than in non-diabetics sera (51/56 vs 1/70) (p<0.001). The diagnostic value for newly-onset IDDM and the high predictive value from the twin study suggest that IA-2 is a major autoantigen for IDDM.